A new decomposition strategy for parallel bonded molecular dynamics
Conference
·
OSTI ID:54401
- Sandia National Laboratories, Albuquerque, NM (United States)
A method is described for parallelizing molecular dynamics (MD) simulations by block-decomposing the matrix of bonded and non-bonded force computations. It is particularly useful for organic simulations (polymers, proteins) because it requires no geometric information about the simulation domain unlike spatial-decomposition methods. Because its communication cost scales as N/{radical}P rather than N as in the all-to-all broadcast or ring-exchange techniques commonly used in this type of MD simulation, larger numbers of processors can be used effectively, yielding greater parallel speed-ups.
- Research Organization:
- Sandia National Laboratory
- DOE Contract Number:
- AC04-76DP00789
- OSTI ID:
- 54401
- Report Number(s):
- DOE/ER/25151--1-Vol.1; CONF-930331--Vol.1
- Country of Publication:
- United States
- Language:
- English
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